The 1st Unified Workshop on Proteome and Metabolome Informatics

Saturday 6th September, 8am registration, 9am - 6pm workshop @ ECCB 2014 


At present there is little contact between metabolomics and proteomics fields at both wet and dry-lab levels, and so key synergies are being lost. A number of packages offer the complete quantification and identification workflow for discovery proteomics and metabolomics but there is little cross-fertilisation between metabolome and proteome informatics groups, despite numerous overlaps and similarities between disciplines. In some ways this is because metabolome and proteome informatics research has originated from different fields (broadly chemometrics and genome bioinformatics, respectively), yet their distinct perspectives have been applied to identical or similar problems.

The integration of quantitative outputs from proteomics and metabolomics for dynamic systems and pathway modelling is reliant on appropriate and accurate statistical handling. Since metabolomics and proteomics data are processed differently, their statistical integration is a significant challenge – there are differing assumptions on biological variation; differing transformations and error distributions from the various processing steps; and subtly different corrections for multiple hypothesis testing. Cross-fertilisation and cross-development of methodology and ideas between disciplines has the prospect of seeding novel and effective new approaches of analysis.

We therefore believe there is a timely opportunity to bring together the informatics communities in metabolomics and proteomics:

  • To underpin existing and to drive new cross-disciplinary collaborations in order to facilitate better statistical integration and therefore better downstream modelling and ultimately biological understanding.
  • To allow these disciplines to better ‘borrow strength’ from each other, improving quantitative workflows at all levels.
  • To impact on researcher mobility due to clearer understanding of the commonality and subtle differences in workflows between disciplines.
  • To support development of joint data exchange and reporting standards for optimal integration of omics data.

Target Audience

This workshop will be of interest to all researchers in proteomics or metabolomics, whether at the wet-lab or informatics level. It will also be of relevance to systems modellers and network biologists who integrate proteomics and metabolomics data and who wish to gain a greater understanding of how upstream processing of this data is performed.

The core aim for this workshop is for there to be an equal proportion of talks on proteome and metabolome informatics. In particular, we will prefer talks that already describe some synergy between the two fields. Speakers are advised to ensure metabolomics concepts are accessible to a proteomics audience, and vice versa.

Call for Contributions

The abstract submission form is here

Abstract submission deadline: Closed for oral presentation, poster abstracts will be accepted until the 1st September 2014.

Submissions for poster only are still invited.


FORUM building
Faculté de Médecine
4, rue Kirschleger


8:00   Registration (W11)

9:00   Welcome - Simon Rogers / Richard Unwin
9:05   Introduction to the new HUPO and ISCB Computational Mass Spectrometry Working Groups - Oliver Kohlbacher, University of Tübingen, Germany

Session 1
 "From spectra to biology - Joint analysis of proteomics and metabolomics data with OpenMS", Oliver Kohlbacher, University of Tübingen, Germany
9:40   "mzMatch: software for metabolomics workflow design and data analysis" - Andris Jankevics, University of Manchester, UK
10:05   "Galaxy: A viable platform for analysing mass spectrometry data?" - Conrad Bessant, Queen Mary University of London, UK

10:30   Coffee break

Session 2
    "Progress in PROCESS for proteomics and metabolomics data standards" - Simon Perkins, University of Liverpool, UK
11:10   “World-wide data exchange in Metabolomics” - Christoph Steinbeck, European Bioinformatics Institute, UK
11:35   "Revisiting hypothetical proteins: Combining ‘omic’ approaches for better functional prediction" - Prashanth Suravajhala, and Bioinformatics.Org

12:00   Lunch
13:00   Poster presenters in attendence

Session 3
   "Proteomics Data, Functional Analysis and Dissemination" - Henning Hermjakob, European Bioinformatics Institute, UK
14:20   "Spatial metabolomics using imaging mass spectrometry" - Theodore Alexandrov, University of Bremen / University of California San Diego / SCiLS
14:45   "Absolute Murder: Informatics challenges for absolute quantitation in proteomics" - Simon Hubbard, University of Manchester, UK
15:10   "‘The importance of metabolite annotation – current software and next steps" - Rick Dunn, University of Birmingham, UK
15:35   "Tsunami or alluvial plain? A primer on dealing with public data", Lennart Martens, Universiteit Gent, Belgium

16:00   Coffee break

Session 4
  "Metabolite identification via multiple kernel learning" - Huibin Shen, Department of Information and Computer Science, Aalto University, Espoo, Finland"
16:45   "A Comparative MS/MS Based Workflow for the Detection of Stable Protein Adducts Induced by Small Molecules" - Markus Müller, Swiss Institute of Bioinformatics, University of Geneva, Switzerland
17:10   "Critical assessment of the elemental isotope definition in mass-spectrometry-based proteomics" - Jürgen Claesen, I-BioStat, UHasselt, Belgium
17:35   "Stronger findings from mass spectral data through hierarchical Bayesian multi-peak modeling" - Tommi Suvitaival, Helsinki Institute for Information Technology HIIT, Finland

18:00   Close


Workshop registration is via the main ECCB'14 registration site. You do not need to register for the main conference to attend the workshop. The fee is 110 € (academic rate) or 60 € (student rate).

Organising Committee

Dr Andrew Dowsey, CADET, University of Manchester
Dr Simon Rogers, School of Computer Science, University of Glasgow
Prof Rainer Breitling, MIB, University of Manchester
Dr Richard Unwin, CADET, University of Manchester


Additional funding for this workshop is provided by BBSRC award BB/L018616/1.